I'm not sure if you are referring to navigation links within the Showkase menu (on all pages including Juicebox gallery pages but not actually within Juicebox galleries themselves) or navigation links within Juicebox galleries (perhaps embedded within image captions).
Juicebox has its own color configuration options (in each gallery page) which are independent of the Showkase color settings (in 'Site -> Customize Theme').
The text color for all Juicebox gallery text can be found in the 'Lite Viewer Options' section of each gallery page.
(You can set default values for all subsequently generated galleries in 'Site -> Customize Viewers' if you like.)
If you change any Showkase colors (in 'Site -> Customize Theme -> Color Palette'), be sure to set 'Site -> Customize Theme -> Color Scheme' to 'custom' to use the custom color palette settings.
I hope these notes help,
However, if you continue to experience difficulties, please post back with the URL to the web page in question and let me know exactly what links you are referring to and I should hopefully be able to let you know how to change their color.